A few days ago I switch all my email accounts from POP to IMAP. As I was already using Poptray to check mail in POP, I kept it for IMAP, with the help of IMAP plugin.
It's working fine except for two things :
- When I try to previes a message in Poptray I get this error message : " Unable to retrieve message. External exception E06D7363",
- When I try to delete a message from Poptray, I also get an error message telling me something about message references that don't match (it's in french ).
The funny thing is that if I switch Poptray language from French to ENglish everything workd fine.

IMAP isn't a very strict standard like POP is, so it doesn't get implemented the same on every server... so try the other IMAP plugins available on the SourceForge pages to see if you get better results with one of them.

Personally I believe, that if your email server allows POP access, that is still the most reliable way to have Poptray check/notify for new email.